A randomized numerical aligner (rNA)

DOI10.1016/j.jcss.2011.12.007zbMath1250.68289OpenAlexW2085332554MaRDI QIDQ1757842

Francesco Vezzi, Alberto Policriti, Alexandru I. Tomescu

Publication date: 6 November 2012

Published in: Journal of Computer and System Sciences (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcss.2011.12.007

zbMATH Keywords

sequencingHamming distanceapproximate string matchingnext generation sequencingshort string aligner

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

Uses Software

• Soap
• Samtools
• BLAT
• PSI-BLAST
• BLAST
• BWA

Cites Work

• Approximate string matching using compressed suffix arrays
• Efficient string matching with k mismatches
• Approximate Boyer-Moore string matching for small alphabets
• A fast string searching algorithm
• Dynamic Text Indexing under String Updates
• Generalized String Matching
• Efficient randomized pattern-matching algorithms
• Fast Pattern Matching in Strings
• Faster algorithms for string matching with k mismatches
• Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
• Combinatorial Pattern Matching
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